Disease(s): UNDIFFERENTIATED SARCOMA (UNDIFS)
Number of RNAseq Samples: 1
| Tumor_Sample_Barcode |
Chromosome |
Start_Position |
Reference_Allele |
Tumor_Seq_Allele2 |
Hugo_Symbol |
VAF |
Variant_Classification |
HGVSp_Short |
| P-0006237-T04-IM6
|
3 |
178917478 |
G |
A |
PIK3CA |
0.270423 |
Missense_Mutation
|
p.G118D |
Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)
Tissue Site: R Gluteal Mass
Days since birth at collection: 8029
| GENE1 |
GENE2 |
DESCRIPTION |
SPAN_READS |
SPLIT_READS |
LEFTBREAK |
RIGHTBREAK |
CALLER_EFFECT |
ANNOT_EFFECT |
CALLER |
NUM_CALLERS |
| MGA |
NUTM1 |
oncogene,cancer,exon-exon |
14 |
19 |
15:42054560:+ |
15:34640170:+ |
in-frame |
in-frame |
FUSIONCATCHER |
3 |
| GENE1 |
GENE2 |
DESCRIPTION |
SPAN_READS |
SPLIT_READS |
LEFTBREAK |
RIGHTBREAK |
CALLER_EFFECT |
ANNOT_EFFECT |
CALLER |
NUM_CALLERS |
| IGH@ |
IL3RA |
known,cancer,m0,multi |
3 |
1 |
14:106913401:- |
X:1449932:+
|
---/intergenic |
---/intergenic |
FUSIONCATCHER |
1 |
Overexpressed Cancer
Genes:
| Gene |
Log Fold Change |
Loc |
Cancers |
| NUTM1 |
7.61806 |
15q14 |
lethal midline
carcinoma |
| OLIG2 |
4.29052 |
21q22.11 |
T-ALL |
| MLF1 |
3.65278 |
3q25.1 |
AML |
| LRIG3 |
2.29114 |
12q14.1 |
NSCLC |
| SFRP4 |
2.16084 |
7p14.1 |
colorectal cancer,
melanoma, SCC, gastric cancer, oesophageal SCC |
Disease: UNDIFFERENTIATED SARCOMA (UNDIFS)
Tissue Site: R Gluteal Mass
Days since birth at collection: 8029
MSISensor HAS NOT BEEN RUN
BBG RAW NORMAL
BBG RAW TUMOR
No Amplifications or Homozygous losses for Oncogenes
or TSGs
| CHR |
START |
GENE |
EFFECT |
cDNA_CHANGE |
PROTEIN_CHANGE |
TARGET_VAF |
REFERENCE_VAF |
REFERENCE_DEPTH |
Oncogene |
TSG |
CCF |
GENE_TPM |
| 3 |
178917478 |
PIK3CA |
non_synonymous_codon
|
c.353G>A |
p.G118D |
0.35 |
0 |
37 |
✔ |
|
0.785316 |
9.70179 |
| CHR |
START |
GENE |
EFFECT |
cDNA_CHANGE |
PROTEIN_CHANGE |
TARGET_VAF |
REFERENCE_VAF |
REFERENCE_DEPTH |
Oncogene |
TSG |
CCF |
GENE_TPM |
| 1 |
35657838
|
SFPQ |
non_synonymous_codon |
c.813G>C
|
p.K271N |
0.42 |
0 |
43 |
|
✔ |
0.930745
|
77.7173
|
| 1 |
43213986
|
LEPRE1 |
non_synonymous_codon |
c.1723G>T
|
p.V575F |
0.37 |
0 |
42 |
|
|
0.843369
|
17.4142
|
| 2 |
103321091
|
SLC9A2 |
non_synonymous_codon |
c.1934G>A
|
p.R645Q |
0.42 |
0 |
47 |
|
|
0.924928
|
1.04438
|
| 2 |
128263132
|
IWS1 |
non_synonymous_codon |
c.347A>G
|
p.H116R |
0.41 |
0 |
31 |
|
|
0.957338
|
8.2394
|
| 2 |
161052875
|
ITGB6 |
non_synonymous_codon |
c.198A>T
|
p.L66F |
0.43 |
0 |
39 |
|
|
0.96284
|
1.06111
|
| 2 |
170050292
|
LRP2 |
non_synonymous_codon |
c.8809G>A
|
p.E2937K
|
0.39 |
0 |
45 |
|
|
0.859149
|
0.014024
|
| 2 |
174820961
|
SP3 |
splice_site_variant |
c.280-1G>A |
p.? |
0.42 |
0 |
27 |
|
|
0.948306
|
19.1651
|
| 3 |
7456718 |
GRM7 |
non_synonymous_codon |
c.1042G>A
|
p.A348T |
0.45 |
0 |
39 |
|
|
0.994606
|
0.444721
|
| 3 |
178917478
|
PIK3CA |
non_synonymous_codon |
c.353G>A
|
p.G118D |
0.35 |
0 |
37 |
✔ |
|
0.785316
|
9.70179
|
| 4 |
57344789
|
SRP72 |
non_synonymous_codon |
c.799G>A
|
p.A267T |
0.48 |
0 |
44 |
|
|
1.0941
|
22.1599
|
| 4 |
135121522
|
PABPC4L
|
non_synonymous_codon |
c.827G>A |
p.S276N
|
0.52 |
0 |
45 |
|
|
1.14016
|
1.92159
|
| 4 |
151000309
|
DCLK2 |
non_synonymous_codon |
c.130C>A |
p.L44I
|
0.5 |
0 |
49 |
|
|
1.14655
|
1.37846
|
| 5 |
140553488
|
PCDHB7
|
non_synonymous_codon |
c.1072G>A |
p.E358K
|
0.27 |
0 |
35 |
|
|
0.606067
|
0.194355
|
| 5 |
175816340
|
HIGD2A
|
non_synonymous_codon |
c.163G>T |
p.A55S
|
0.47 |
0 |
49 |
|
|
1.04405
|
15.4683
|
| 5 |
179251300
|
SQSTM1
|
non_synonymous_codon |
c.650G>A |
p.R217H
|
0.43 |
0 |
66 |
|
|
0.97943
|
38.4831
|
| 6 |
100965942
|
ASCC3 |
non_synonymous_codon |
c.5852T>C |
p.I1951T
|
0.47 |
0 |
45 |
|
|
1.04988
|
11.0422
|
| 6 |
126080617
|
HEY2 |
non_synonymous_codon |
c.683C>T |
p.T228M
|
0.41 |
0 |
43 |
|
|
0.907476
|
0.037566
|
| 6 |
144070126
|
PHACTR2
|
non_synonymous_codon |
c.219A>C |
p.L73F
|
0.41 |
0 |
44 |
|
|
0.920948
|
10.2718
|
| 7 |
21695506
|
DNAH11
|
non_synonymous_codon |
c.5001C>A |
p.D1667E
|
0.33 |
0 |
41 |
|
|
1.03822
|
4.17408
|
| 7 |
39649386
|
YAE1D1
|
non_synonymous_codon |
c.422G>A |
p.S141N
|
0.33 |
0 |
46 |
|
|
1.042
|
13.5995
|
| 7 |
92763691
|
SAMD9L
|
non_synonymous_codon |
c.1594C>A |
p.L532I
|
0.29 |
0 |
38 |
|
|
0.938198
|
4.40977
|
| 7 |
121756802
|
AASS |
non_synonymous_codon |
c.779T>A |
p.V260E
|
0.28 |
0 |
54 |
|
|
0.92394
|
4.26067
|
| 8 |
24250832
|
ADAMDEC1
|
non_synonymous_codon |
c.265C>G |
p.L89V
|
0.51 |
0 |
46 |
|
|
1.18862
|
0.203587
|
| 9 |
33347710
|
NFX1 |
non_synonymous_codon |
c.2474A>G |
p.K825R
|
0.057 |
0 |
42 |
|
|
0.127645
|
11.2156
|
| 9 |
101552725
|
ANKS6 |
non_synonymous_codon |
c.523C>A |
p.P175T
|
0.4 |
0 |
60 |
|
|
0.873361
|
2.71904
|
| 10 |
75457455
|
AGAP5 |
non_synonymous_codon |
c.59A>C
|
p.Q20P
|
0.058 |
0 |
47 |
|
|
0.131399
|
7.04692
|
| 11 |
118263544
|
UBE4A |
non_synonymous_codon |
c.3029A>G |
p.D1010G
|
0.46 |
0 |
42 |
|
|
1.02634
|
10.2147
|
| 11 |
123865313
|
OR10G6
|
non_synonymous_codon |
c.556C>T |
p.R186W
|
0.37 |
0 |
53 |
|
|
0.806646
|
0 |
| 11 |
128781700
|
KCNJ5 |
non_synonymous_codon |
c.532G>A |
p.V178I
|
0.39 |
0 |
42 |
✔ |
|
0.866843
|
0.55527
|
| 12 |
47628898
|
PCED1B
|
non_synonymous_codon |
c.52G>A
|
p.V18M
|
0.26 |
0 |
40 |
|
|
0.804425
|
0.202481
|
| 12 |
113836935
|
SDS |
non_synonymous_codon |
c.175C>T |
p.H59Y
|
0.34 |
0 |
60 |
|
|
0.762757
|
0.408721
|
| 14 |
70925531
|
ADAM21
|
non_synonymous_codon |
c.1315A>T |
p.T439S
|
0.058 |
0 |
33 |
|
|
0.129495
|
0.024045
|
| 15 |
35196649
|
AQR |
non_synonymous_codon |
c.1889A>T |
p.D630V
|
0.26 |
0 |
48 |
|
|
0.843096
|
15.4681
|
| 16 |
23767024
|
CHP2 |
non_synonymous_codon |
c.110C>T |
p.A37V
|
0.067 |
0 |
34 |
|
|
0.151811
|
1.1927
|
| 16 |
66956040
|
RRAD |
non_synonymous_codon |
c.866A>G |
p.N289S
|
0.42 |
0 |
44 |
|
|
0.957338
|
0.200276
|
| 16 |
69148514
|
HAS3 |
non_synonymous_codon |
c.1007G>A |
p.R336H
|
0.11 |
0 |
34 |
|
|
0.239994
|
0.046976
|
| 16 |
87735456
|
FLJ00104
|
non_synonymous_codon |
c.665G>T |
p.W222L
|
0.36 |
0 |
50 |
|
|
0.814185
|
0.142219
|
| 18 |
14852452
|
ANKRD30B
|
non_synonymous_codon |
c.4152C>A |
p.N1384K
|
0.78 |
0 |
36 |
|
|
0.952398
|
0.050045
|
| 19 |
35996863
|
DMKN |
non_synonymous_codon |
c.1064T>C |
p.F355S
|
0.39 |
0 |
39 |
|
|
0.869794
|
0.214859
|
| 20 |
34055250
|
CEP250
|
non_synonymous_codon |
c.721C>T |
p.R241W
|
0.43 |
0 |
42 |
|
|
0.962527
|
4.94952
|
| 20 |
49571815
|
DPM1 |
non_synonymous_codon |
c.169A>G |
p.N57D
|
0.45 |
0 |
40 |
|
|
1.0052
|
10.9651
|
| 22 |
20709527
|
FAM230A
|
non_synonymous_codon |
c.1259A>C |
p.N420T
|
0.52 |
0.07 |
43 |
|
|
0.714298
|
0.061481
|
| X |
77529113
|
CYSLTR1
|
non_synonymous_codon |
c.131T>C |
p.V44A
|
0.8 |
0 |
18 |
|
|
1.77285
|
5.42012
|
| X |
79698692
|
FAM46D
|
non_synonymous_codon |
c.654G>C |
p.L218F
|
0.91 |
0 |
31 |
|
|
2.0565
|
0 |
| CHR |
START |
GENE |
EFFECT |
cDNA_CHANGE |
PROTEIN_CHANGE |
TARGET_VAF |
REFERENCE_VAF |
REFERENCE_DEPTH |
Oncogene |
TSG |
CCF |
TARGET_VAFCORRECT_VAF |
NORMAL_VAFCORRECT_VAF |
GENE_TPM |
| 3 |
8809437 |
OXTR |
frameshift_variant |
c.436delC
|
p.R146fs*61
|
0.385 |
0 |
57 |
|
|
0.94936
|
0.42 |
0 |
0.279616
|
| 4 |
87731112
|
PTPN13 |
frameshift_variant |
c.7290_7300delGGGATTAATCA |
p.G2431fs*4
|
0.382 |
0 |
50 |
|
✔ |
0.865809
|
0.41 |
0 |
16.6623
|
| 4 |
140811578
|
MAML3 |
inframe_codon_loss |
c.1009_1011delAAG |
p.K337delK
|
0.317 |
0 |
52 |
|
|
0.883513
|
0.4 |
0 |
5.69363
|
Rearranged Tumor Suppressor Genes:
| gene1 |
gene2 |
svclass |
brass_score |
| EPHB2 |
BACH2 |
translocation |
45 |
| AGAP1 |
HDAC4 |
inversion |
43 |
| _ |
HDAC4 |
inversion |
29 |
| _ |
NF2 |
translocation |
43 |
| TERT |
TERT |
deletion |
5 |
| gene1 |
gene2 |
svclass |
brass_score |
| AGAP1 |
HDAC4 |
inversion |
43 |
| _ |
HDAC4 |
inversion |
29 |
| TERT |
TERT |
deletion |
5 |
| COL4A3BP |
ROS1 |
translocation |
37 |
| KSR2 |
KSR2 |
tandem-duplication
|
46 |
|
SNVS |
Coding SNVS |
INDELS |
Coding INDELS |
#Coding/Mb |
#Muts/Mb |
REARR |
|
I-H-108333-T2-2-D1-1 |
3575 |
44 |
490 |
3 |
1.57 |
1.40 |
61 |